Predicting ADME properties in silico: methods and models

Size: px
Start display at page:

Download "Predicting ADME properties in silico: methods and models"

Transcription

1 DDT Vol. 7, No. 11 (Suppl.), 2002 information biotechnology supplement reviews Predicting ADME properties in silico: methods and models Darko Butina, Matthew D. Segall and Katrina Frankcombe Unfavourable absorption, distribution, metabolism and elimination (ADME) properties have been identified as a major cause of failure for candidate molecules in drug development. Consequently, there is increasing interest in the early prediction of ADME properties, with the objective of increasing the success rate of compounds reaching development. This review explores in silico approaches and selected published models for predicting ADME properties from chemical structure alone. In particular, we provide a comparison of methods based on pattern recognition to identify correlations between molecular descriptors and ADME properties, structural models based on classical molecular mechanics and quantum mechanical techniques for modelling chemical reactions. Darko Butina and Katrina Frankcombe ArQule (UK) 127 Science Park Milton Road Cambridge UK CB4 6DG *Matthew D. Segall ArQule (UK) and Cavendish Laboratory University of Cambridge tel: fax: * msegall@ arqule.com The number of research papers, reviews and commercial products relating to the prediction of absorption, distribution, metabolism and elimination (ADME) properties of pharmaceutical compounds has increased dramatically in recent years [1 3]. The reason for this is that ADME properties have been recognized as a major reason for the failure of drug candidates in the late stages of drug development, with a large financial impact on the cost of R&D in the pharmaceutical industry [4]. The ability to model ADME properties of molecules will facilitate the drug discovery process in several ways. Compounds for highthroughput screening (HTS) are, at present, chosen primarily on the basis of potency. The ability to simultaneously filter these molecules in silico for suitable ADME properties will result in higher quality leads emerging from HTS campaigns. Probably the most widely used ADME model is Lipinski s rule of 5, which is used in the pharmaceutical industry to filter out compounds likely to be purely absorbed through the human intestine, based on four simple rules related to molecular properties [5]. In silico models of ADME can also be used to test individual molecules or chemical libraries as license-in opportunities, evaluating their suitability as potential drug molecules. During lead optimization, the ability to predict the effect of a proposed structural modification in silico, before compound synthesis, will result in fewer redesign synthesize test cycles. This is most powerful if a model can provide guidance regarding the structural modifications that will improve a property. Modelling ADME properties ADME properties are difficult to model for several reasons. The quality of experimental data varies enormously and is often limited in quantity and chemical diversity. This is especially true in the case of data obtained directly from humans. In addition, ADME properties such as oral bioavailability, human intestinal absorption (HIA) and metabolic stability arise from multiple physiological mechanisms, which make them difficult to model with traditional quantitative structure activity relationship (QSAR) approaches. To deal with the biological complexity from which ADME properties arise, a range of different techniques must be applied. A schematic illustrating this spectrum is shown in Fig. 1. Models of ADME properties are most commonly based on empirical approaches such as QSAR. These techniques can be applied with great efficiency to large numbers of molecules, but require a significant quantity of high quality data from which to deduce a relationship between structure and activity. With increasing understanding of the structural basis of the mechanisms giving rise to ADME properties on a molecular level, approaches based on atomistic modelling will /02/$ see front matter 2002 Elsevier Science Ltd. All rights reserved. PII: S (02) S83

2 reviews information biotechnology supplement DDT Vol. 7, No. 11 (Suppl.), 2002 Empirical Fast Non-transferable QSAR Homology modelling Classical molecular dynamics Semiempirical (e.g. INDO) Density functional theory Correlated wave-function Figure 1. The spectrum of approaches to modelling absorption, distribution, metabolism and elimination (ADME) properties. Trends across the scale are indicated by the words above. Advantages are highlighted in green and drawbacks in red. Methods to the left are empirical in nature, based on parameters fitted to large numbers of data points, whereas those to the right are based on first principle approaches. Empirical approaches tend to be faster, and able to make predictions many orders of magnitude faster than the first principle approaches which require large computational resources. Although empirical approaches may be applied to predict a wide range of properties, a large quantity of high-quality experimental data for each must be used for parameterization. By contrast, the first principle approaches are based on fundamental physical principles, and hence may be applied to a wide range of problems without re-parameterization. become more widely applied. These techniques, based on molecular or quantum mechanics, are more computationally intensive, but make quantitative predictions based on general physical principles. The following sections will explore these approaches in greater detail and give examples of their application to the prediction of ADME properties of compounds. Pattern recognition methods The term pattern recognition is used to describe any mathematical or statistical method that might be used to detect or reveal patterns in data. These identify a QSAR, relating a set of descriptors describing chemical structure (denoted X) to the observed activity (Y), which in this case is the ADME property of interest. The parameters of the model relating Y to X are fitted from a set of molecules for which experimental data are available.this is commonly referred to as a training set. In general, models based on fitting approaches can only make reliable predictions for molecules similar to those in the training set the chemical space of the model. Although a prediction for a molecule significantly different from the training set might be correct, a source of uncontrolled error is introduced. The diversity of the molecules for which experimental data are available is the primary limiting factor in the applicability of models based on empirical fitting techniques. Another difficulty in the fitting procedure is the avoidance of over-fitting.the fit of a model to the data in the training set might be improved by increasing the complexity of the model. First principles Slow Transferable Exact solution DDT: InfoBiotech supplement However, improving the fit to the training set will eventually lead to a failure of the model to generalize to molecules that are not in this set. One approach for avoiding this is cross-correlation, whereby one or more molecules are omitted from the training set, and the model is refitted using the remaining molecules. Predictions for the omitted molecules are then made with the resulting model and the process repeated until predictions have been made for all of the molecules in the training set. The correlation coefficient between the predicted and experimental values is calculated (commonly referred to as Q 2 ) and compared with that for the model trained on the entire training set (R 2 ). No significant difference should be observed if the model is not over-fitted. A preferable approach, where sufficient data are available, is to use an independent test set of molecules to which the model is never fitted. If the model is not over-fitted, the correlation between predicted and experimental values for the test set should be comparable to that of the training set. Several approaches can be used to train a QSAR model. The most common of these are briefly described in the following section. More details can be found in the references given [6 18]. Statistical regression Statistical regression is primarily a tool for deriving linear models between X and Y, and has been applied in many ADME models, including the calculation of whole molecule physicochemical properties such as solubility and lipophilicity. Multiple linear regression (MLR) is one of the oldest methods used to find a linear relationship between the observed activities and a set of descriptors [6]. A problem with this approach is that, as a rule of thumb, 4 5 examples (i.e. molecules) are required for each descriptor used. In addition, descriptors that are correlated or have skewed distributions a common problem with chemical structures will give poor regression models. Partial least squares (PLS) has become a standard in this area. It overcomes most of the known problems with MLR, for example enabling the use of correlated descriptors [7,8]. A large number of descriptors can be used, even larger than the number of molecules in the training set, and the descriptors with the most influence on the model can be conveniently identified. Simple non-linearities in the QSAR, for example, involving an exponent or logarithm of a descriptor value, can be easily included. More complex non-linear relationships can be treated by non-linear PLS [9]. However, other approaches are more suitable to modelling complex non-linear QSAR. S84

3 DDT Vol. 7, No. 11 (Suppl.), 2002 information biotechnology supplement reviews Classification methods Where multiple biological mechanisms contribute to determining an ADME property, or a strongly non-linear relationship between the descriptors and property exists, it is often not possible to make a numerical prediction of that molecular property. An example of this is oral bioavailability, which is determined by absorption through the gut wall, possible active efflux by transporters such as P-glycoprotein, and metabolism in both the gut wall and liver. In these cases, classification methods are often employed that assign the property of a molecule to one of two or more classes, rather than predicting a numerical value. Several techniques may be used to achieve this, including: Linear discriminant analysis (LDA) calculates discriminant functions or hyperplanes that partition the space of chemical descriptors to give the best separation between different classes [10]. Decision trees create a branching structure in which the branch taken at each intersection is determined by a rule relating to the descriptors for a molecule. Each leaf of the tree is assigned to a class [11]. k Nearest Neighbours (knn) identifies the k molecules in the training set that lie closest to the molecule for which the prediction is being made [12]. Distance is assessed using a measure of structural similarity, such as the Tanimoto index or an Euclidian distance in the space of descriptors [13].The class of the unknown molecule is assigned by a voting procedure among the k nearest neighbours. Artificial neural networks Artificial neural networks (ANNs) is a pattern recognition approach inspired by the capabilities of the CNS [14]. A network of artificial neurones is trained to reproduce Y given a set of inputs X for a training set of molecules. This network can then be used to make predictions for molecules for which Y is unknown. ANNs are a powerful approach for fitting non-linear functions relating X and Y. However, it is often difficult to decode the final model to identify the changes to molecular structure needed to obtain a desired property. Also, ANNs have a tendency to memorize rather than learn and are particularly susceptible to over-fitting, especially if the training data is noisy.techniques such as regularization can help to limit over-fitting, by penalizing overly complex functions during fitting [15]. Genetic algorithms Genetic algorithms (GAs) are a class of heuristic search algorithms inspired by the mechanism of evolution [16].The set of parameters defining a model relating Y to X represents the DNA for an initial population with appropriate genetic diversity. A combination of mutation and breeding within this population is used iteratively to evolve the population and the fittest of each generation is selected for the next iteration. The fitness of each model in the population is judged by the agreement between the predictions of the model and the data in a training set. A separate test-set guards against over-fitting. GAs are sometimes used as an approach to training and designing ANNs [17]. Other forms of GA, such as genetic programming [18], can also generate non-linear relationships between descriptors and properties. GAs are good at finding different solutions to the same problem, but the quality of the solutions are very sensitive to the parameters controlling cross-over and mutation rates. Molecular and quantum mechanics When an ADME property is influenced by the interaction of a compound with a molecular system, typically an enzyme or transporter, it is often possible to model directly the interaction at an atomistic level, enabling quantitative predictions to be made. Chemical reactions, such as enzyme catalysis, require quantum mechanical (QM) simulations. However, the structural features of a complex formed by an interaction of a ligand with a binding site can be modelled using a molecular mechanics (MM) approach. In this approach, the atoms are treated with a classical ball and stick approach. The principal advantage of MM lies in the computational efficiency of the method. However, the atomic interactions must be empirically parameterized for specific sets of atoms and it can be difficult to determine if the assumptions implicit in the parameterization are violated, which would introduce a source of uncontrolled error into the simulation. The aim of QM methods is to obtain an approximate solution of the Schrödinger equation. Various approximations have been invoked for tractability, giving rise to ab initio and semiempirical techniques.the most rigorous, and consequently the most computationally demanding, is ab initio theory. Ab initio methods use rigorous approximations borne from general physical principles alone and require no experimental parameters. As such, their quantitative application is not limited to specific types of system [19 21]. By contrast, experimental parameterization or neglect of the most time-consuming components of the Schrödinger equation gave rise to semiempirical methods. Although not as reliable and versatile as ab initio techniques, such algorithms can be routinely applied to much larger systems [22 24]. To simulate the interaction of a ligand with a binding site, information regarding the structural basis for the interaction must be available. The lack of 3D structural data for proteins relevant to ADME processes is the main reason for the limited application of these techniques in this field. The exception to this is cytochrome P450 (CYP450), for which several crystal S85

4 reviews information biotechnology supplement DDT Vol. 7, No. 11 (Suppl.), 2002 structures are available for bacterial (see for example [25 27]), as well as a single mammalian P450, CYP2C5 [28]. From these, homology models have been derived for some human P450s, including CYP2D6 [29] and CYP 3A4 [30]. As structural information on other drug metabolizing enzymes and transporters becomes available, the application of these techniques will become more widespread. ADME models Many models for ADME properties have been published, or are available commercially. Suppliers of commercial models include ArQule (Woburn, MA, USA) (formerly Camitro Corporation), Simulations Plus (Lancaster, CA, USA), Advanced Chemistry Development (Toronto, Ont., Canada), Amedis (Cambridge, UK), Accelrys (San Diego, CA, USA) and Lion Bioscience (San Diego, CA, USA). Although this review does not give an exhaustive list of ADME models, an illustrative list of properties that have been modelled, including references for examples of published models, is described in the next section. Whole molecule properties Some physicochemical properties of molecules, although useful in their own right, provide important molecular descriptors for use in models of ADME properties. These models are typically derived via regression methods. In particular: Solubility. The Klopman solubility model is frequently quoted and widely used [31].The training set for this model excluded molecules with charged atoms such as basic nitrogens or carboxylic acids. As many drug molecules contain charged atoms, the applicability of this model is limited. A model generated using an ANN has also been published by Liu and So [32]. Acidity or basicity (pka/pkb). This property is very important, as it determines the protonation state of the compound at different ph values. Hydrophobicity. This is based on measured octanol-water partition (logp) data. A commonly referenced model for logp is that of Moriguchi et al. [33]. This is a regression model built on a training set of 1230 compounds, for which it achieves a correlation of Human intestinal absorption Wessel et al. have reported a model based on 76 compounds with reported HIA data, using GA with an ANN scoring function [34]. A standard error of 16% was obtained for the test set of 10 molecules. Clark reports the use of polar surface area (PSA) to create a classification model to separate poor (<10%) from wellabsorbed ( 10%) compounds [35], using the same data set as reported by Wessel et al. [34]. Egan et al. published a model for HIA based on PSA and logp descriptors alone [36]. This classification model was found to be between 74% and 92% accurate for different sets of molecules. Abraham and his collaborators have recently reported a model based on a comprehensive HIA dataset [37]. Using Abraham descriptors, described in the same paper, the authors report R 2 = 0.74 when trained on the whole set. However, the authors also highlight the fact that the training set is heavily biased towards well-absorbed compounds (over 30% absorbed). Blood brain barrier Young et al. have reported a model based on only six H 2 antagonists for which C brain /C blood were determined [38]. Abraham et al. have built a model based on 45 data points and experimentally determined descriptors, including the hydrogenbonding capability of the molecule [39]. The use of descriptors that can only be obtained by an experimental method implies serious limitations in its use. However, a recent paper that calculates Abraham descriptors has made them available to the rest of the computational chemistry community [40]. A model based on 3D molecular descriptors and a discriminant PLS approach was published by Crivori et al. [41]. The resulting model was found to correctly predict more than 90% of the available blood brain barrier (BBB) permeation data. Human bioavailability Hirono et al. [42] have built a model based on 188 drug molecules using the fuzzy adaptive least squares method [43]. The model was validated by leave one out cross validation, not an independent test set. Yoshida and Topliss have reported a non-linear model, based on 232 compounds as their training set and 40 as a test set [44]. All the compounds have human bioavailability (%F) data reported, but the set was divided into four classes and discriminant functions were developed to separate the classes. Andrews et al. have reported a model based on stepwise regression and 591 compounds [45]. Poor bioavailability predictions were false in only 3% of cases, but 53% of predictions of high bioavailability were incorrect. Metabolism Korzekwa et al. successfully applied semi-empirical QM methods to prediction of the regioselectivity of CYP450-mediated hydroxylation [46]. Using simple models for the haem-oxygenthiolate molecule, the group modelled hydrogen abstraction from different carbons for a series of substrates. A correlation was observed between the stability of the product radicals with respect to their parents and the regioselectivity of CYP450 hydroxylation. S86

5 DDT Vol. 7, No. 11 (Suppl.), 2002 information biotechnology supplement reviews Harris and Loew studied the regioselectivities of metabolism of several substrates by P450 cam, a bacterial CYP450 from pseudomonas putida, using dynamical MM (molecular dynamics) simulations based on crystal structures of the substrate enzyme complexes [47]. The aim of this study was to identify the sites of hydrogen abstraction from the substrate, thought to be the rate-limiting step in product formation. These simulations do not take into account the reactivity of each site on the substrate, which is calculated using QM approaches as described above. However, the results from MD identify those hydrogen atoms that are accessible to the reactive ferryl oxygen centre.the calculated regioselectivites agree well with those observed experimentally. Similar simulations, based on homology models, have been performed for human CYP3A4 [48] and CYP2C9 [49] enzymes. Concluding remarks No single approach can be used to predict the full range of ADME properties that are desired. A challenge in this field is to identify the technique that is most suitable for modelling the property under investigation. In fact, a combination of two or more models for the same property, based on different principles, can give higher confidence in the results obtained for which they agree or identify areas of uncertainty where they differ. At present, models are available both in the literature and from commercial sources for the prediction of ADME properties such as solubility, HIA, bioavailability, BBB penetration and regioselectivity of CYP450 metabolism. Within the next year, the range of models will expand to include metabolism by other drug-metabolizing enzymes, active transport by proteins such as P-glycoprotein, plasma protein binding and renal and biliary clearance, among others. This will achieve coverage of the major ADME properties affecting the pharmacokinetics of compounds. Physiologically based pharmacokinetic (PBPK) simulations have been developed (see for example [50,51]) that predict PK properties such as plasma concentration as a function of time, which, in turn, will yield parameters such as half-life and clearance. Existing simulations usually rely on compound ADME data obtained in vitro or in vivo. However, the results of predictive ADME models will be used as inputs to PBPK simulations, enabling accurate in silico prediction of PK properties from compound structure alone within the next two to three years. With this, compounds with unsuitable PK will be eliminated early in drug discovery and those designed with optimal properties will proceed into development [3]. References 1 Ekins, S. and Rose, J. (2002) In silico ADME/Tox: the state of the art. J. Mol. Graph. Model. 20, Ekins, S. et al. (2000) Progress in predicting human ADME parameters in silico. J. Pharmacol.Toxicol. Meth. 44, Selick, H.E. et al. (2002) The emerging importance of predictive ADME simulation in drug discovery. Drug Discov.Today 7, Dimasi, J.A. (2001) Risks in new drug development: approval success rates for investigational drugs. Clin. Pharmacol.Ther. 69, Lipinski, C.A. et al. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23, Draper, N.R. and Smith, H. (1981) Applied Regression Analysis, John Wiley & Sons 7 Geladi, P. (1992) Wold, Herman, the father of PLS. Chemometr. Intell. Lab. Syst. 15, R7 R8 8 Wold, S. et al. (1999) PLS in chemistry. In The Encyclopedia of Computational Chemistry (Schleyer, P.V.R. et al., eds.), pp , John Wiley & Sons 9 Wold, S. (1992) Nonlinear partial least squares modelling II. Spline inner relation. Chemometr. Intell. Lab. Syst. 14, Anderson,T.W. (1984) An Introduction to Multivariate Statistics. John Wiley & Sons 11 Quinlan, R. (1986) Induction of decision trees. Machine Learning 1, Shultz,T.W. and Moulton, M.P. (1985) Structure toxicity relationships of selected naphthalene derivatives II. Principal components analysis. Bull. Environ. Contam.Toxicol. 34, Dean, P.M. (1994) Molecular Similarity in Drug Design. Kluwer Academic Publishers 14 Hopfield, J.J. (1982) Neural networks and physical systems with emergent collective computational abilities. Proc. Natl.Acad. Sci. U. S.A. 79, Burden, F.R. et al. (2000) Use of automatic relevance determination in QSAR studies using Bayesian neural networks. J. Chem. Inf. Comput. Sci. 40, Goldberg, D.E. (1988) Genetic Algorithms in Search, Optimisation and Machine Learning. Addison-Wesley 17 Yao, X. (1999) Evolving artificial neural networks. Proc. IEEE 87, Koza, J.R. (1992) Genetic Programming: On the Programming of Computers by Means of Natural Selection. The MIT Press 19 Hehre, W.J. et al. (1986) Ab initio Molecular Orbital Theory, John Wiley & Sons 20 Ragavachari, K. and Curtiss, L.A. (1995) Evaluation of bond energies to chemical accuracy by quantum chemical techniques. In Modern Electronic Structure Theory (Yarkony, D.R., ed.), pp ,World Scientific Press 21 Curtiss, L.A. and Ragavachari, K. (1995) Calculation of accurate bond energies, electron affinities, and ionization energies. In Quantum Mechanical Electronic Structure Calculations with Chemical Accuracy: Understanding Chemical Reactivity (Langhoff, S.R., ed.), pp , Kluwer Academic Press 22 Dewar, M.J. and Thiel, W. (1977) Ground states of molecules. 38.The MNDO method. Approximations and parameters. J.Am. Chem. Soc. 99, Stewart, J.J.P. (1989) Optimization of parameters for semiempirical methods. 2. Applications. J. Comput. Chem. 10, S87

6 reviews information biotechnology supplement DDT Vol. 7, No. 11 (Suppl.), Clarke,T. (1985) A Handbook of Computational Chemistry:A Practical Guide to Chemical Structure and Energy Calculations, John Wiley & Sons 25 Poulos,T.L. et al. (1987) High-resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 195, Hasemann, C.A. et al. (1994) Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution. J. Mol. Biol. 236, Ravichandran, K.G. et al. (1993) Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450s. Science 261, Williams, P.A. et al. (2000) Microsomal cytochrome P450 2C5: comparison to microbial P450s and unique features. J. Inorg. Biochem. 81, Lewis, D.F. et al. (1997) Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: structural studies on specific CYP2D6 substrate metabolism. Xenobiotica 27, Lewis, D.F. et al. (1996) Molecular modelling of CYP3A4 from an alignment with CYP102: identification of key interactions between putative active site residues and CYP3A-specific chemicals. Xenobiotica 26, Klopman, G. et al. (1992) Estimation of aqueous solubility of organic molecules by the group contribution approach. Application to the study of biodegradation. J. Chem. Inf. Comput. Sci. 32, Liu, R. and So, S.S. (2001) Development of quantitative structure property relationship models for early ADME evaluation in drug discovery. 1. Aqueous solubility. J. Chem. Inf. Comput. Sci. 41, Moriguchi, I. et al. (1992) Simple method of calculating octanol/water partition coefficient. Chem. Pharm. Bull. (Tokyo) 40, Wessel, M.D. et al. (1998) Prediction of human intestinal absorption of drug compounds from molecular structure. J. Chem. Inf. Comput. Sci. 38, Clark, D.E. (1999) Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 1. Prediction of intestinal absorption. J. Pharm. Sci. 88, Egan,W.J. et al. (2000) Prediction of drug absorption using multivariate statistics. J. Med. Chem. 43, Zhao,Y.H. et al. (2001) Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure activity relationship (QSAR) with the Abraham descriptors. J. Pharm. Sci. 90, Young, R.C. et al. (1988) Development of a new physicochemical model for brain penetration and its application to the design of centrally acting H2 receptor histamine antagonists. J. Med. Chem. 31, Abraham, M.H. et al. (1994) Hydrogen bonding. 33. Factors that influence the distribution of solutes between blood and brain. J. Pharm. Sci. 83, Platts, J.A. et al. (1999) Estimation of molecular linear free energy relation descriptors using a group contribution approach. J. Chem. Inf. Comput. Sci. 39, Crivori, P. et al. (2000) Predicting blood brain barrier permeation from three-dimensional molecular structure. J. Med. Chem. 43, Hirono, S. et al. (1994) Non-congeneric structure pharmacokinetic property correlation studies using fuzzy adaptive least-squares: oral bioavailability. Biol. Pharm. Bull. 17, Moriguchi, I. et al. (1990) Fuzzy adaptive least squares and its use in quantitative structure activity relationships. Chem. Pharm. Bull. (Tokyo) 38, Yoshida, F. and Topliss, J.G. (2000) QSAR model for drug human oral bioavailability. J. Med. Chem. 43, Andrews, C.W. et al. (2000) Predicting human oral bioavailability of a compound: development of a novel quantitative structure bioavailability relationship. Pharm. Res. 17, Korzekwa, K.R. et al. (1996) Electronic models of Cytochrome P450 oxidations. In Biological Reactive Intermediates V (Snyder, R., ed.), pp , Plenum Press 47 Harris, D. and Loew, G. (1995) Prediction of regiospecific hydroxylation of camphor analogs by cytochrome-p450(cam). J.Am. Chem. Soc. 117, Kuhn, B. et al. (2001) Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. J. Med. Chem. 44, Payne,V.A. et al. (1999) Homology modeling and substrate binding study of human CYP2C9 enzyme. Proteins 37, Oliver, R.E. et al. (2001) A whole-body physiologically based pharmacokinetic model incorporating dispersion concepts: short and long time characteristics. J. Pharmacokinet. Biopharm. 28, Norris, D.A. et al. (2000) Development of predictive pharmacokinetic simulation models for drug discovery. J Control. Release 65, Information Biotechnology To purchase additional copies of this supplement, please contact: Stacey Sheekey Commercial Sales Department, Current Trends, Elsevier Science London, 84 Theobalds Road, London, UK WC1X 8RR tel: fax: stacey.sheekey@bmn.com S88

Quantum Mechanical Models of P450 Metabolism to Guide Optimization of Metabolic Stability

Quantum Mechanical Models of P450 Metabolism to Guide Optimization of Metabolic Stability Quantum Mechanical Models of P450 Metabolism to Guide Optimization of Metabolic Stability Optibrium Webinar 2015, June 17 2015 Jonathan Tyzack, Matthew Segall, Peter Hunt Optibrium, StarDrop, Auto-Modeller

More information

Translating Methods from Pharma to Flavours & Fragrances

Translating Methods from Pharma to Flavours & Fragrances Translating Methods from Pharma to Flavours & Fragrances CINF 27: ACS National Meeting, New Orleans, LA - 18 th March 2018 Peter Hunt, Edmund Champness, Nicholas Foster, Tamsin Mansley & Matthew Segall

More information

Introduction to Chemoinformatics and Drug Discovery

Introduction to Chemoinformatics and Drug Discovery Introduction to Chemoinformatics and Drug Discovery Irene Kouskoumvekaki Associate Professor February 15 th, 2013 The Chemical Space There are atoms and space. Everything else is opinion. Democritus (ca.

More information

Plan. Lecture: What is Chemoinformatics and Drug Design? Description of Support Vector Machine (SVM) and its used in Chemoinformatics.

Plan. Lecture: What is Chemoinformatics and Drug Design? Description of Support Vector Machine (SVM) and its used in Chemoinformatics. Plan Lecture: What is Chemoinformatics and Drug Design? Description of Support Vector Machine (SVM) and its used in Chemoinformatics. Exercise: Example and exercise with herg potassium channel: Use of

More information

Computational Methods and Drug-Likeness. Benjamin Georgi und Philip Groth Pharmakokinetik WS 2003/2004

Computational Methods and Drug-Likeness. Benjamin Georgi und Philip Groth Pharmakokinetik WS 2003/2004 Computational Methods and Drug-Likeness Benjamin Georgi und Philip Groth Pharmakokinetik WS 2003/2004 The Problem Drug development in pharmaceutical industry: >8-12 years time ~$800m costs >90% failure

More information

In silico pharmacology for drug discovery

In silico pharmacology for drug discovery In silico pharmacology for drug discovery In silico drug design In silico methods can contribute to drug targets identification through application of bionformatics tools. Currently, the application of

More information

molecules ISSN

molecules ISSN Molecules 2004, 9, 1004-1009 molecules ISSN 1420-3049 http://www.mdpi.org Performance of Kier-Hall E-state Descriptors in Quantitative Structure Activity Relationship (QSAR) Studies of Multifunctional

More information

Bridging the Dimensions:

Bridging the Dimensions: Bridging the Dimensions: Seamless Integration of 3D Structure-based Design and 2D Structure-activity Relationships to Guide Medicinal Chemistry ACS Spring National Meeting. COMP, March 13 th 2016 Marcus

More information

Structural biology and drug design: An overview

Structural biology and drug design: An overview Structural biology and drug design: An overview livier Taboureau Assitant professor Chemoinformatics group-cbs-dtu otab@cbs.dtu.dk Drug discovery Drug and drug design A drug is a key molecule involved

More information

Advanced Medicinal Chemistry SLIDES B

Advanced Medicinal Chemistry SLIDES B Advanced Medicinal Chemistry Filippo Minutolo CFU 3 (21 hours) SLIDES B Drug likeness - ADME two contradictory physico-chemical parameters to balance: 1) aqueous solubility 2) lipid membrane permeability

More information

Structure-Activity Modeling - QSAR. Uwe Koch

Structure-Activity Modeling - QSAR. Uwe Koch Structure-Activity Modeling - QSAR Uwe Koch QSAR Assumption: QSAR attempts to quantify the relationship between activity and molecular strcucture by correlating descriptors with properties Biological activity

More information

Early Stages of Drug Discovery in the Pharmaceutical Industry

Early Stages of Drug Discovery in the Pharmaceutical Industry Early Stages of Drug Discovery in the Pharmaceutical Industry Daniel Seeliger / Jan Kriegl, Discovery Research, Boehringer Ingelheim September 29, 2016 Historical Drug Discovery From Accidential Discovery

More information

Plan. Day 2: Exercise on MHC molecules.

Plan. Day 2: Exercise on MHC molecules. Plan Day 1: What is Chemoinformatics and Drug Design? Methods and Algorithms used in Chemoinformatics including SVM. Cross validation and sequence encoding Example and exercise with herg potassium channel:

More information

ADME SCREENING OF NOVEL 1,4-DIHYDROPYRIDINE DERIVATIVES

ADME SCREENING OF NOVEL 1,4-DIHYDROPYRIDINE DERIVATIVES ITERATIAL JURAL F RESEARC I PARMACY AD CEMISTRY Available online at www.ijrpc.com Research Article ADME SCREEIG F VEL 1,4-DIYDRPYRIDIE DERIVATIVES A. Asma samaunnisa 1*, CS. Venkataramana 1 and V Madhavan

More information

Hydrogen Bonding & Molecular Design Peter

Hydrogen Bonding & Molecular Design Peter Hydrogen Bonding & Molecular Design Peter Kenny(pwk.pub.2008@gmail.com) Hydrogen Bonding in Drug Discovery & Development Interactions between drug and water molecules (Solubility, distribution, permeability,

More information

COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS

COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS DRUG DEVELOPMENT Drug development is a challenging path Today, the causes of many diseases (rheumatoid arthritis, cancer, mental diseases, etc.)

More information

Receptor Based Drug Design (1)

Receptor Based Drug Design (1) Induced Fit Model For more than 100 years, the behaviour of enzymes had been explained by the "lock-and-key" mechanism developed by pioneering German chemist Emil Fischer. Fischer thought that the chemicals

More information

Applying Bioisosteric Transformations to Predict Novel, High Quality Compounds

Applying Bioisosteric Transformations to Predict Novel, High Quality Compounds Applying Bioisosteric Transformations to Predict Novel, High Quality Compounds Dr James Chisholm,* Dr John Barnard, Dr Julian Hayward, Dr Matthew Segall*, Mr Edmund Champness*, Dr Chris Leeding,* Mr Hector

More information

Using AutoDock for Virtual Screening

Using AutoDock for Virtual Screening Using AutoDock for Virtual Screening CUHK Croucher ASI Workshop 2011 Stefano Forli, PhD Prof. Arthur J. Olson, Ph.D Molecular Graphics Lab Screening and Virtual Screening The ultimate tool for identifying

More information

JCICS Major Research Areas

JCICS Major Research Areas JCICS Major Research Areas Chemical Information Text Searching Structure and Substructure Searching Databases Patents George W.A. Milne C571 Lecture Fall 2002 1 JCICS Major Research Areas Chemical Computation

More information

Easier and Better Exploitation of PhysChem Properties in Medicinal Chemistry

Easier and Better Exploitation of PhysChem Properties in Medicinal Chemistry www.acdlabs.com Easier and Better Exploitation of PhysChem Properties in Medicinal Chemistry Dr. Sanjivanjit K. Bhal Advanced Chemistry Development, Inc. (ACD/Labs) Evolution of MedChem

More information

ASSESSING THE DRUG ABILITY OF CHALCONES USING IN- SILICO TOOLS

ASSESSING THE DRUG ABILITY OF CHALCONES USING IN- SILICO TOOLS Page109 IJPBS Volume 5 Issue 1 JAN-MAR 2015 109-114 Research Article Pharmaceutical Sciences ASSESSING THE DRUG ABILITY OF CHALCONES USING IN- SILICO TOOLS Department of Pharmaceutical Chemistry, Institute

More information

Next Generation Computational Chemistry Tools to Predict Toxicity of CWAs

Next Generation Computational Chemistry Tools to Predict Toxicity of CWAs Next Generation Computational Chemistry Tools to Predict Toxicity of CWAs William (Bill) Welsh welshwj@umdnj.edu Prospective Funding by DTRA/JSTO-CBD CBIS Conference 1 A State-wide, Regional and National

More information

Practical QSAR and Library Design: Advanced tools for research teams

Practical QSAR and Library Design: Advanced tools for research teams DS QSAR and Library Design Webinar Practical QSAR and Library Design: Advanced tools for research teams Reservationless-Plus Dial-In Number (US): (866) 519-8942 Reservationless-Plus International Dial-In

More information

Quantitative Structure-Activity Relationship (QSAR) computational-drug-design.html

Quantitative Structure-Activity Relationship (QSAR)  computational-drug-design.html Quantitative Structure-Activity Relationship (QSAR) http://www.biophys.mpg.de/en/theoretical-biophysics/ computational-drug-design.html 07.11.2017 Ahmad Reza Mehdipour 07.11.2017 Course Outline 1. 1.Ligand-

More information

Machine learning for ligand-based virtual screening and chemogenomics!

Machine learning for ligand-based virtual screening and chemogenomics! Machine learning for ligand-based virtual screening and chemogenomics! Jean-Philippe Vert Institut Curie - INSERM U900 - Mines ParisTech In silico discovery of molecular probes and drug-like compounds:

More information

Gaussian Processes: We demand rigorously defined areas of uncertainty and doubt

Gaussian Processes: We demand rigorously defined areas of uncertainty and doubt Gaussian Processes: We demand rigorously defined areas of uncertainty and doubt ACS Spring National Meeting. COMP, March 16 th 2016 Matthew Segall, Peter Hunt, Ed Champness matt.segall@optibrium.com Optibrium,

More information

Nonlinear QSAR and 3D QSAR

Nonlinear QSAR and 3D QSAR onlinear QSAR and 3D QSAR Hugo Kubinyi Germany E-Mail kubinyi@t-online.de HomePage www.kubinyi.de onlinear Lipophilicity-Activity Relationships drug receptor Possible Reasons for onlinear Lipophilicity-Activity

More information

FRAUNHOFER IME SCREENINGPORT

FRAUNHOFER IME SCREENINGPORT FRAUNHOFER IME SCREENINGPORT Design of screening projects General remarks Introduction Screening is done to identify new chemical substances against molecular mechanisms of a disease It is a question of

More information

Statistical concepts in QSAR.

Statistical concepts in QSAR. Statistical concepts in QSAR. Computational chemistry represents molecular structures as a numerical models and simulates their behavior with the equations of quantum and classical physics. Available programs

More information

ADMET property estimation, oral bioavailability predictions, SAR elucidation, & QSAR model building software www.simulations-plus.com +1-661-723-7723 What is? is an advanced computer program that enables

More information

PHYSIO-CHEMICAL PROPERTIES OF THE DRUG. It is the interaction of the drug with its environment

PHYSIO-CHEMICAL PROPERTIES OF THE DRUG. It is the interaction of the drug with its environment PYSIO-CEMICAL PROPERTIES OF TE DRUG It is the interaction of the drug with its environment Reducing the complexity Biological process in drug action Dissolution of drug in gastrointestinal fluids Absorption

More information

Data Quality Issues That Can Impact Drug Discovery

Data Quality Issues That Can Impact Drug Discovery Data Quality Issues That Can Impact Drug Discovery Sean Ekins 1, Joe Olechno 2 Antony J. Williams 3 1 Collaborations in Chemistry, Fuquay Varina, NC. 2 Labcyte Inc, Sunnyvale, CA. 3 Royal Society of Chemistry,

More information

Flow of information in a drug discovery pipeline. 7th lecture Modern Methods in Drug Discovery WS16/17 1

Flow of information in a drug discovery pipeline. 7th lecture Modern Methods in Drug Discovery WS16/17 1 Flow of information in a drug discovery pipeline 7th lecture Modern Methods in Drug Discovery WS16/17 1 eadmet prediction early Absorption Distribution Metabolism Elimination Toxicology Pharmacokinetic

More information

Exploring the chemical space of screening results

Exploring the chemical space of screening results Exploring the chemical space of screening results Edmund Champness, Matthew Segall, Chris Leeding, James Chisholm, Iskander Yusof, Nick Foster, Hector Martinez ACS Spring 2013, 7 th April 2013 Optibrium,

More information

In Silico Investigation of Off-Target Effects

In Silico Investigation of Off-Target Effects PHARMA & LIFE SCIENCES WHITEPAPER In Silico Investigation of Off-Target Effects STREAMLINING IN SILICO PROFILING In silico techniques require exhaustive data and sophisticated, well-structured informatics

More information

Retrieving hits through in silico screening and expert assessment M. N. Drwal a,b and R. Griffith a

Retrieving hits through in silico screening and expert assessment M. N. Drwal a,b and R. Griffith a Retrieving hits through in silico screening and expert assessment M.. Drwal a,b and R. Griffith a a: School of Medical Sciences/Pharmacology, USW, Sydney, Australia b: Charité Berlin, Germany Abstract:

More information

Multi-Parameter Optimization: Identifying high quality compounds with a balance of properties

Multi-Parameter Optimization: Identifying high quality compounds with a balance of properties Multi-Parameter Optimization: Identifying high quality compounds with a balance of properties Matthew D Segall Optibrium Ltd., 7226 Cambridge Research Park, Beach Drive, Cambridge, CB25 9TL, UK Email:

More information

Pre-processing feature selection for improved C&RT models for oral absorption

Pre-processing feature selection for improved C&RT models for oral absorption Pre-processing feature selection for improved C&RT models for oral absorption Danielle Newby a, Alex. A. Freitas b, Taravat Ghafourian a,c * a Medway School of Pharmacy, Universities of Kent and Greenwich,

More information

Rapid Application Development using InforSense Open Workflow and Daylight Technologies Deliver Discovery Value

Rapid Application Development using InforSense Open Workflow and Daylight Technologies Deliver Discovery Value Rapid Application Development using InforSense Open Workflow and Daylight Technologies Deliver Discovery Value Anthony Arvanites Daylight User Group Meeting March 10, 2005 Outline 1. Company Introduction

More information

Towards Physics-based Models for ADME/Tox. Tyler Day

Towards Physics-based Models for ADME/Tox. Tyler Day Towards Physics-based Models for ADME/Tox Tyler Day Overview Motivation Application: P450 Site of Metabolism Application: Membrane Permeability Future Directions and Applications Motivation Advantages

More information

QSAR Modeling of ErbB1 Inhibitors Using Genetic Algorithm-Based Regression

QSAR Modeling of ErbB1 Inhibitors Using Genetic Algorithm-Based Regression APPLICATION NOTE QSAR Modeling of ErbB1 Inhibitors Using Genetic Algorithm-Based Regression GAINING EFFICIENCY IN QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS ErbB1 kinase is the cell-surface receptor

More information

Introduction. OntoChem

Introduction. OntoChem Introduction ntochem Providing drug discovery knowledge & small molecules... Supporting the task of medicinal chemistry Allows selecting best possible small molecule starting point From target to leads

More information

2009 Optibrium Ltd. Optibrium, STarDrop, Auto-Modeler and Glowing Molecule are trademarks of Optibrium Ltd.

2009 Optibrium Ltd. Optibrium, STarDrop, Auto-Modeler and Glowing Molecule are trademarks of Optibrium Ltd. Enabling Interactive Multi-Objective Optimization for Drug Discovery Scientists Matthew Segall matt.segall@optibrium.com Lorentz Workshop Optimizing Drug Design 2009 Optibrium Ltd. Optibrium, STarDrop,

More information

DivCalc: A Utility for Diversity Analysis and Compound Sampling

DivCalc: A Utility for Diversity Analysis and Compound Sampling Molecules 2002, 7, 657-661 molecules ISSN 1420-3049 http://www.mdpi.org DivCalc: A Utility for Diversity Analysis and Compound Sampling Rajeev Gangal* SciNova Informatics, 161 Madhumanjiri Apartments,

More information

Virtual Libraries and Virtual Screening in Drug Discovery Processes using KNIME

Virtual Libraries and Virtual Screening in Drug Discovery Processes using KNIME Virtual Libraries and Virtual Screening in Drug Discovery Processes using KNIME Iván Solt Solutions for Cheminformatics Drug Discovery Strategies for known targets High-Throughput Screening (HTS) Cells

More information

Computational Chemistry in Drug Design. Xavier Fradera Barcelona, 17/4/2007

Computational Chemistry in Drug Design. Xavier Fradera Barcelona, 17/4/2007 Computational Chemistry in Drug Design Xavier Fradera Barcelona, 17/4/2007 verview Introduction and background Drug Design Cycle Computational methods Chemoinformatics Ligand Based Methods Structure Based

More information

Correspondence should be addressed to M. G. Shambhu;

Correspondence should be addressed to M. G. Shambhu; Medicinal Chemistry Volume 2013, Article ID 495134, 6 pages http://dx.doi.org/10.1155/2013/495134 Research Article The Development of Models Based on Linear and Nonlinear Multivariate Methods to Predict

More information

Notes of Dr. Anil Mishra at 1

Notes of Dr. Anil Mishra at   1 Introduction Quantitative Structure-Activity Relationships QSPR Quantitative Structure-Property Relationships What is? is a mathematical relationship between a biological activity of a molecular system

More information

Comparing Multi-Label Classification Methods for Provisional Biopharmaceutics Class Prediction

Comparing Multi-Label Classification Methods for Provisional Biopharmaceutics Class Prediction Comparing Multi-Label Classification Methods for Provisional Biopharmaceutics Class Prediction Danielle Newby a, Alex. A. Freitas b, Taravat Ghafourian a,c* a Medway School of Pharmacy, Universities of

More information

Application integration: Providing coherent drug discovery solutions

Application integration: Providing coherent drug discovery solutions Application integration: Providing coherent drug discovery solutions Mitch Miller, Manish Sud, LION bioscience, American Chemical Society 22 August 2002 Overview 2 Introduction: exploring application integration

More information

Relative Drug Likelihood: Going beyond Drug-Likeness

Relative Drug Likelihood: Going beyond Drug-Likeness Relative Drug Likelihood: Going beyond Drug-Likeness ACS Fall National Meeting, August 23rd 2012 Matthew Segall, Iskander Yusof Optibrium, StarDrop, Auto-Modeller and Glowing Molecule are trademarks of

More information

Dispensing Processes Profoundly Impact Biological, Computational and Statistical Analyses

Dispensing Processes Profoundly Impact Biological, Computational and Statistical Analyses Dispensing Processes Profoundly Impact Biological, Computational and Statistical Analyses Sean Ekins 1, Joe Olechno 2 Antony J. Williams 3 1 Collaborations in Chemistry, Fuquay Varina, NC. 2 Labcyte Inc,

More information

The Changing Requirements for Informatics Systems During the Growth of a Collaborative Drug Discovery Service Company. Sally Rose BioFocus plc

The Changing Requirements for Informatics Systems During the Growth of a Collaborative Drug Discovery Service Company. Sally Rose BioFocus plc The Changing Requirements for Informatics Systems During the Growth of a Collaborative Drug Discovery Service Company Sally Rose BioFocus plc Overview History of BioFocus and acquisition of CDD Biological

More information

Chemogenomic: Approaches to Rational Drug Design. Jonas Skjødt Møller

Chemogenomic: Approaches to Rational Drug Design. Jonas Skjødt Møller Chemogenomic: Approaches to Rational Drug Design Jonas Skjødt Møller Chemogenomic Chemistry Biology Chemical biology Medical chemistry Chemical genetics Chemoinformatics Bioinformatics Chemoproteomics

More information

Dr. Sander B. Nabuurs. Computational Drug Discovery group Center for Molecular and Biomolecular Informatics Radboud University Medical Centre

Dr. Sander B. Nabuurs. Computational Drug Discovery group Center for Molecular and Biomolecular Informatics Radboud University Medical Centre Dr. Sander B. Nabuurs Computational Drug Discovery group Center for Molecular and Biomolecular Informatics Radboud University Medical Centre The road to new drugs. How to find new hits? High Throughput

More information

Reaxys Medicinal Chemistry Fact Sheet

Reaxys Medicinal Chemistry Fact Sheet R&D SOLUTIONS FOR PHARMA & LIFE SCIENCES Reaxys Medicinal Chemistry Fact Sheet Essential data for lead identification and optimization Reaxys Medicinal Chemistry empowers early discovery in drug development

More information

Comparing Multilabel Classification Methods for Provisional Biopharmaceutics Class Prediction

Comparing Multilabel Classification Methods for Provisional Biopharmaceutics Class Prediction pubs.acs.org/molecularpharmaceutics Comparing Multilabel Classification Methods for Provisional Biopharmaceutics Class Prediction Danielle Newby, Alex. A. Freitas, and Taravat Ghafourian*,, Medway School

More information

PHARMA SCIENCE MONITOR AN INTERNATIONAL JOURNAL OF PHARMACEUTICAL SCIENCES

PHARMA SCIENCE MONITOR AN INTERNATIONAL JOURNAL OF PHARMACEUTICAL SCIENCES PHARMA SCIENCE MONITOR AN INTERNATIONAL JOURNAL OF PHARMACEUTICAL SCIENCES LIPOPHILICITY OF FEW CHROMEN-2-ONES AND CHROMENE-2-THIONES BY HYPERCHEM 7.0 AND ALOGPS 2.1 P. Jayanthi* and P. Lalitha Department

More information

CH MEDICINAL CHEMISTRY

CH MEDICINAL CHEMISTRY CH 458 - MEDICINAL CHEMISTRY SPRING 2011 M: 5:15pm-8 pm Sci-1-089 Prerequisite: Organic Chemistry II (Chem 254 or Chem 252, or equivalent transfer course) Instructor: Dr. Bela Torok Room S-1-132, Science

More information

An Integrated Approach to in-silico

An Integrated Approach to in-silico An Integrated Approach to in-silico Screening Joseph L. Durant Jr., Douglas. R. Henry, Maurizio Bronzetti, and David. A. Evans MDL Information Systems, Inc. 14600 Catalina St., San Leandro, CA 94577 Goals

More information

Applications of multi-class machine

Applications of multi-class machine Applications of multi-class machine learning models to drug design Marvin Waldman, Michael Lawless, Pankaj R. Daga, Robert D. Clark Simulations Plus, Inc. Lancaster CA, USA Overview Applications of multi-class

More information

Synthetic organic compounds

Synthetic organic compounds Synthetic organic compounds for research and drug discovery Compounds for TS Fragment libraries Target-focused libraries Chemical building blocks Custom synthesis Drug discovery services Contract research

More information

Computational Models for the Prediction of Intestinal Membrane Permeability

Computational Models for the Prediction of Intestinal Membrane Permeability Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy 247 Computational Models for the Prediction of Intestinal Membrane Permeability BY PATRIC STENBERG ACTA UNIVERSITATIS UPSALIENSIS

More information

Comparison of log P/D with bio-mimetic properties

Comparison of log P/D with bio-mimetic properties Comparison of log P/D with bio-mimetic properties Klara Valko Bio-Mimetic Chromatography Consultancy for Successful Drug Discovery Solvation process First we need to create a cavity Solute molecule Requires

More information

Targeted Covalent Inhibitors: A Risk-Benefit Perspective

Targeted Covalent Inhibitors: A Risk-Benefit Perspective Targeted Covalent Inhibitors: A Risk-Benefit Perspective 2014 AAPS Annual Meeting and Exposition San Diego, CA, November 4, 2014 Thomas A. Baillie School of Pharmacy University of Washington Seattle, WA

More information

A Tiered Screen Protocol for the Discovery of Structurally Diverse HIV Integrase Inhibitors

A Tiered Screen Protocol for the Discovery of Structurally Diverse HIV Integrase Inhibitors A Tiered Screen Protocol for the Discovery of Structurally Diverse HIV Integrase Inhibitors Rajarshi Guha, Debojyoti Dutta, Ting Chen and David J. Wild School of Informatics Indiana University and Dept.

More information

CNS-Targeted Library

CNS-Targeted Library CNS-Targeted Library Medicinal and Computational Chemistry Dept., ChemDiv, Inc., 6605 Nancy Ridge Drive, San Diego, CA 92121 USA, Service: +1 877 ChemDiv, Tel: +1 858-794-4860, Fax: +1 858-794-4931, Email:

More information

1. (18) Multiple choice questions. Please place your answer on the line preceding each question.

1. (18) Multiple choice questions. Please place your answer on the line preceding each question. CEM 5720 ame KEY Exam 2 ctober 21, 2015 Read all questions carefully and attempt those questions you are sure of first. Remember to proof your work; art work carries as much importance as written responses.

More information

bcl::cheminfo Suite Enables Machine Learning-Based Drug Discovery Using GPUs Edward W. Lowe, Jr. Nils Woetzel May 17, 2012

bcl::cheminfo Suite Enables Machine Learning-Based Drug Discovery Using GPUs Edward W. Lowe, Jr. Nils Woetzel May 17, 2012 bcl::cheminfo Suite Enables Machine Learning-Based Drug Discovery Using GPUs Edward W. Lowe, Jr. Nils Woetzel May 17, 2012 Outline Machine Learning Cheminformatics Framework QSPR logp QSAR mglur 5 CYP

More information

Computational chemical biology to address non-traditional drug targets. John Karanicolas

Computational chemical biology to address non-traditional drug targets. John Karanicolas Computational chemical biology to address non-traditional drug targets John Karanicolas Our computational toolbox Structure-based approaches Ligand-based approaches Detailed MD simulations 2D fingerprints

More information

Machine Learning Concepts in Chemoinformatics

Machine Learning Concepts in Chemoinformatics Machine Learning Concepts in Chemoinformatics Martin Vogt B-IT Life Science Informatics Rheinische Friedrich-Wilhelms-Universität Bonn BigChem Winter School 2017 25. October Data Mining in Chemoinformatics

More information

Stephen McDonald, Mark D. Wrona, Jeff Goshawk Waters Corporation, Milford, MA, USA INTRODUCTION

Stephen McDonald, Mark D. Wrona, Jeff Goshawk Waters Corporation, Milford, MA, USA INTRODUCTION Combined with a Deep Understanding of Complex Metabolic Routes to Increase Efficiency in the Metabolite Identification Search Stephen McDonald, Mark D. Wrona, Jeff Goshawk Waters Corporation, Milford,

More information

COMBINATORIAL CHEMISTRY: CURRENT APPROACH

COMBINATORIAL CHEMISTRY: CURRENT APPROACH COMBINATORIAL CHEMISTRY: CURRENT APPROACH Dwivedi A. 1, Sitoke A. 2, Joshi V. 3, Akhtar A.K. 4* and Chaturvedi M. 1, NRI Institute of Pharmaceutical Sciences, Bhopal, M.P.-India 2, SRM College of Pharmacy,

More information

Exploring the black box: structural and functional interpretation of QSAR models.

Exploring the black box: structural and functional interpretation of QSAR models. EMBL-EBI Industry workshop: In Silico ADMET prediction 4-5 December 2014, Hinxton, UK Exploring the black box: structural and functional interpretation of QSAR models. (Automatic exploration of datasets

More information

Lead- and drug-like compounds: the rule-of-five revolution

Lead- and drug-like compounds: the rule-of-five revolution Drug Discovery Today: Technologies Vol. 1, No. 4 2004 DRUG DISCOVERY TODAY TECHNOLOGIES Editors-in-Chief Kelvin Lam Pfizer, Inc., USA Henk Timmerman Vrije Universiteit, The Netherlands Lead profiling Lead-

More information

QSAR in Green Chemistry

QSAR in Green Chemistry QSAR in Green Chemistry Activity Relationship QSAR is the acronym for Quantitative Structure-Activity Relationship Chemistry is based on the premise that similar chemicals will behave similarly The behavior/activity

More information

based prediction algorithm for tissue to plasma partition coefficients

based prediction algorithm for tissue to plasma partition coefficients Development of a correlation based and a decision tree based prediction algorithm for tissue to plasma partition coefficients by Yejin Yun A thesis presented to the University of Waterloo in fulfillment

More information

Advances in Multi-parameter Optimisation Methods for de Novo Drug Design

Advances in Multi-parameter Optimisation Methods for de Novo Drug Design Advances in Multi-parameter Optimisation Methods for de Novo Drug Design Abstract Introduction A high quality drug must achieve a balance of physicochemical and ADME properties, safety and potency against

More information

Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism using Quantum Mechanical Simulations

Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism using Quantum Mechanical Simulations Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism using Quantum Mechanical Simulations Jonathan D. Tyzack, Peter A. Hunt, Matthew D. Segall Optibrium Ltd., 7221 Cambridge Research

More information

QSAR Modeling of Human Liver Microsomal Stability Alexey Zakharov

QSAR Modeling of Human Liver Microsomal Stability Alexey Zakharov QSAR Modeling of Human Liver Microsomal Stability Alexey Zakharov CADD Group Chemical Biology Laboratory Frederick National Laboratory for Cancer Research National Cancer Institute, National Institutes

More information

QMRF identifier (JRC Inventory): QMRF Title: QSAR model for blood-brain barrier (BBB) partition Printing Date:

QMRF identifier (JRC Inventory): QMRF Title: QSAR model for blood-brain barrier (BBB) partition Printing Date: QMRF identifier (JRC Inventory): QMRF Title: QSAR model for blood-brain barrier (BBB) partition Printing Date:21.01.2010 1.QSAR identifier 1.1.QSAR identifier (title): QSAR model for blood-brain barrier

More information

Metabolite Identification and Characterization by Mining Mass Spectrometry Data with SAS and Python

Metabolite Identification and Characterization by Mining Mass Spectrometry Data with SAS and Python PharmaSUG 2018 - Paper AD34 Metabolite Identification and Characterization by Mining Mass Spectrometry Data with SAS and Python Kristen Cardinal, Colorado Springs, Colorado, United States Hao Sun, Sun

More information

Accelerating the Metabolite Identification Process Using High Resolution Q-TOF Data and Mass-MetaSite Software

Accelerating the Metabolite Identification Process Using High Resolution Q-TOF Data and Mass-MetaSite Software Accelerating the Metabolite Identification Process Using High Resolution Q-TOF Data and Mass-MetaSite Software Application ote Drug discovery and development: Metabolite Identifi cation Authors Yuqin Dai,

More information

Predicting volume of distribution with decision tree-based regression methods using predicted tissue:plasma partition coefficients

Predicting volume of distribution with decision tree-based regression methods using predicted tissue:plasma partition coefficients Freitas et al. Journal of Cheminformatics (2015) 7:6 DOI 10.1186/s13321-015-0054-x RESEARCH ARTICLE Open Access Predicting volume of distribution with decision tree-based regression methods using predicted

More information

Alkane/water partition coefficients and hydrogen bonding. Peter Kenny

Alkane/water partition coefficients and hydrogen bonding. Peter Kenny Alkane/water partition coefficients and hydrogen bonding Peter Kenny (pwk.pub.2008@gmail.com) Neglect of hydrogen bond strength: A recurring theme in medicinal chemistry Rule of 5 Rule of 3 Scoring functions

More information

PROVIDING CHEMINFORMATICS SOLUTIONS TO SUPPORT DRUG DISCOVERY DECISIONS

PROVIDING CHEMINFORMATICS SOLUTIONS TO SUPPORT DRUG DISCOVERY DECISIONS 179 Molecular Informatics: Confronting Complexity, May 13 th - 16 th 2002, Bozen, Italy PROVIDING CHEMINFORMATICS SOLUTIONS TO SUPPORT DRUG DISCOVERY DECISIONS CARLETON R. SAGE, KEVIN R. HOLME, NIANISH

More information

Application of Raman Spectroscopy for Detection of Aflatoxins and Fumonisins in Ground Maize Samples

Application of Raman Spectroscopy for Detection of Aflatoxins and Fumonisins in Ground Maize Samples Application of Raman Spectroscopy for Detection of Aflatoxins and Fumonisins in Ground Maize Samples Kyung-Min Lee and Timothy J. Herrman Office of the Texas State Chemist, Texas A&M AgriLife Research

More information

Quantitative structure activity relationship and drug design: A Review

Quantitative structure activity relationship and drug design: A Review International Journal of Research in Biosciences Vol. 5 Issue 4, pp. (1-5), October 2016 Available online at http://www.ijrbs.in ISSN 2319-2844 Research Paper Quantitative structure activity relationship

More information

Novel Methods for Graph Mining in Databases of Small Molecules. Andreas Maunz, Retreat Spitzingsee,

Novel Methods for Graph Mining in Databases of Small Molecules. Andreas Maunz, Retreat Spitzingsee, Novel Methods for Graph Mining in Databases of Small Molecules Andreas Maunz, andreas@maunz.de Retreat Spitzingsee, 05.-06.04.2011 Tradeoff Overview Data Mining i Exercise: Find patterns / motifs in large

More information

Solvent & geometric effects on non-covalent interactions

Solvent & geometric effects on non-covalent interactions Solvent & geometric effects on non-covalent interactions Scott L. Cockroft PhysChem Forum 10, Syngenta, Jealott s Hill, 23 rd March 11 QSAR & Physical Organic Chemistry Quantifiable Physicochemical Properties

More information

MM-GBSA for Calculating Binding Affinity A rank-ordering study for the lead optimization of Fxa and COX-2 inhibitors

MM-GBSA for Calculating Binding Affinity A rank-ordering study for the lead optimization of Fxa and COX-2 inhibitors MM-GBSA for Calculating Binding Affinity A rank-ordering study for the lead optimization of Fxa and COX-2 inhibitors Thomas Steinbrecher Senior Application Scientist Typical Docking Workflow Databases

More information

Virtual affinity fingerprints in drug discovery: The Drug Profile Matching method

Virtual affinity fingerprints in drug discovery: The Drug Profile Matching method Ágnes Peragovics Virtual affinity fingerprints in drug discovery: The Drug Profile Matching method PhD Theses Supervisor: András Málnási-Csizmadia DSc. Associate Professor Structural Biochemistry Doctoral

More information

Chemoinformatics and Drug Discovery

Chemoinformatics and Drug Discovery Molecules 2002, 7, 566-600 molecules ISSN 1420-3049 http://www.mdpi.org Review: Chemoinformatics and Drug Discovery Jun Xu* and Arnold Hagler Discovery Partners International, Inc., 9640 Towne Center Drive,

More information

MULTIVARIATE PATTERN RECOGNITION FOR CHEMOMETRICS. Richard Brereton

MULTIVARIATE PATTERN RECOGNITION FOR CHEMOMETRICS. Richard Brereton MULTIVARIATE PATTERN RECOGNITION FOR CHEMOMETRICS Richard Brereton r.g.brereton@bris.ac.uk Pattern Recognition Book Chemometrics for Pattern Recognition, Wiley, 2009 Pattern Recognition Pattern Recognition

More information

The use of Design of Experiments to develop Efficient Arrays for SAR and Property Exploration

The use of Design of Experiments to develop Efficient Arrays for SAR and Property Exploration The use of Design of Experiments to develop Efficient Arrays for SAR and Property Exploration Chris Luscombe, Computational Chemistry GlaxoSmithKline Summary of Talk Traditional approaches SAR Free-Wilson

More information

Cheminformatics Role in Pharmaceutical Industry. Randal Chen Ph.D. Abbott Laboratories Aug. 23, 2004 ACS

Cheminformatics Role in Pharmaceutical Industry. Randal Chen Ph.D. Abbott Laboratories Aug. 23, 2004 ACS Cheminformatics Role in Pharmaceutical Industry Randal Chen Ph.D. Abbott Laboratories Aug. 23, 2004 ACS Agenda The big picture for pharmaceutical industry Current technological/scientific issues Types

More information

Computational Materials Science. Krishnendu Biswas CY03D0031

Computational Materials Science. Krishnendu Biswas CY03D0031 Computational Materials Science Krishnendu Biswas CY03D0031 Outline Introduction Fundamentals How to start Application examples Softwares Sophisticated methods Summary References 2 Introduction Uses computers

More information

Principles of Drug Design

Principles of Drug Design Advanced Medicinal Chemistry II Principles of Drug Design Tentative Course Outline Instructors: Longqin Hu and John Kerrigan Direct questions and enquiries to the Course Coordinator: Longqin Hu I. Introduction

More information

Molecular Interactions F14NMI. Lecture 4: worked answers to practice questions

Molecular Interactions F14NMI. Lecture 4: worked answers to practice questions Molecular Interactions F14NMI Lecture 4: worked answers to practice questions http://comp.chem.nottingham.ac.uk/teaching/f14nmi jonathan.hirst@nottingham.ac.uk (1) (a) Describe the Monte Carlo algorithm

More information